Questions tagged [phylogeny]

Phylogeny is the study of relationships between items (organisms, concepts, etc); typically represented by phylogenetic trees. Such trees may simply reflect evolutionary relationships; or their branches may be scaled according to some measure of evolutionary distance, such as accumulated mutations or time.

Phylogeny is the study of relationships between items (organisms, concepts, etc). The primary use of phylogeny is in systematics, the inference of evolutionary history from morphological and/or molecular data; this typically requires computational methods. Relationships are often depicted as trees, whose branches may scale according to an aspect of evolutionary distance, such as number of mutations, or time. When temporal and/or geographic data are available, phylodynamic or phylogeographic analyses can be performed.

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Make a consensus tree from several tree using Bio.phylo

I'm interested in 4 housekeeping genes in enterobacter bacteria genome's. So I have my housekeeping genes, I made a blast on NR and download the aligned sequences. I made phylogenetic trees using MEGA7 software with Maximum Likehood method.…
Nono_sad
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How to rotate nodes of phylogeny in R without overlapping?

I'm trying to make nice figures for my phylogenies in R (I'm working my way up to using R for analyses). The trees have been made in Garli and MrBayes. The Garli (maximum likelihood) trees have been behaving with all the typical ape, phytools, and…
Brigette Z
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Using python 3.x how can I pass a Tree object from ete3 to DendroPy without writing to file

I'm using the ete3 package in python to build phylogenetic trees from data I've generated with a stochastic model and it works well. I have previously written these trees to newick format and then used another script, with the package Dendropy, to…
cancerconnector
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ggtree change radius scale

I am trying to create a phylogenetic tree with ggtree. I am having trouble resizing the centre of the tree so that the symbols on the edge representing my sequences are not overlapping and increasing the radius so that the branch lengths are not as…
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How to use categorical vectors in ape (r) for phylogenetic independent contrasts

I have been performing phylogenetically independent contrasts of several ecological variables for the cat phylogeny, using the ape package in R, and I was wondering how this can be done using categorical values. Here is how it works using…
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Distance between species in the Open Tree of Life

Greetings and Salutations, I'm trying to find the relative distance to other species in the Open Tree of Life (OTOL). I'm using the phytools R package's fastDist() function to generate a count between branches of the tree. However, the function…
coatless
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Phylogenetic Tree - how to create a branch by species matrix?

Working with a phylogenetic tree in R, I would like to create a matrix which indicates if each branch of the tree (B1 to B8) is associated with each species (A to E), where 1s indicate that the branch is associated. (Shown below) The R function…
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Biopython Phylogenetic Tree Edit labels in SVG file

I try to have the full length label into my phylogenetic tree using the python library Biopython with the Phylo.draw(). I import my newick file format, I draw it, and I save it: from Bio import Phylo import pylab f = 'path/to/my/file' tree =…
ybz
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Join 2 trees using Python (dendroPy or other libraries)

I am working on phylogenies by using Python libraries (Bio.Phylo and DendroPy). I have to import 2 trees in Newick format (this is obviously not the difficult part) and join them together, more precisely I have to add one tree at one tip/leaf of…
Erica Fary
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Find tips in R tree newick format

I imported a Newick tree into R with ape (read.tree). The problem is that when I plot the tree the labels overlap because there are 1000 tips. I am not copying the tree in here because it is a very long expression. Is there a way to see which…
janbrei
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"rerootable" purely functional tree data structure

I recently purchased Inferring Phylogenies by Joseph Felsenstein, which is a great book about mathematical and computational methods for inferring phylogenetic trees, and have been playing around with implementing some of the algorithms it…
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Phylogenetic Tree Coloring

I have created a phylogenetic tree of a bunch on enzyme sequences I have. I have it in a simple format with only scores displayed and no coloring. Now the sequences I have are Restriction enzymes and each of them have a motif. I want to color the…
letsc
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Link tip labels to phylogenetic tree using dots

I'm trying to produce a non-ultrametric tree using the ape package in R and the function plot.phylo(). I'm struggling to find any documentation on how to keep the tip label vertically aligned on their left edge and with a series of dots (variable…
Rambatino
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igraph loses internal node structure from phylogenetic tree (as.igraph() tree conversion)

I've converted a phylogenetic tree to an igraph graph object in R. The conversion is pretty straight forward. (I've even written my own) x <- read.tree(treeName) #library(ape) xg <- as.igraph(x) #library(igraph) xn <- as.network(x) …
laemtao
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Parsing through sequence output- Python

I have this data from sequencing a bacterial community. I know some basic Python and am in the midst of completing the codecademy tutorial. For practical purposes, please think of OTU as another word for "species" Here is an example of the raw…
user3277533
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